A novel approach to evaluating cancer driver gene mutation densities: cytoskeleton-related gene candidates
TJ Fawcett, ML Parry, G Blanck - Cancer Genomics & …, 2015 - cgp.iiarjournals.org
Background: Oncoprotein genes are over-represented in statically defined, low mutation-
frequency fractions of cancer genome atlas (TCGA) datasets, consistent with a higher driver …
frequency fractions of cancer genome atlas (TCGA) datasets, consistent with a higher driver …
OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes
D Tamborero, A Gonzalez-Perez… - Bioinformatics, 2013 - academic.oup.com
Motivation: Gain-of-function mutations often cluster in specific protein regions, a signal that
those mutations provide an adaptive advantage to cancer cells and consequently are …
those mutations provide an adaptive advantage to cancer cells and consequently are …
The FABRIC cancer portal: A ranked catalogue of gene selection in tumors over the human coding genome
Contemporary catalogues of cancer driver genes rely primarily on high mutation rates as
evidence for gene selection in tumors. Here, we present The Functional Alteration Bias …
evidence for gene selection in tumors. Here, we present The Functional Alteration Bias …
An integrative somatic mutation analysis to identify pathways linked with survival outcomes across 19 cancer types
Motivation: Identification of altered pathways that are clinically relevant across human
cancers is a key challenge in cancer genomics. Precise identification and understanding of …
cancers is a key challenge in cancer genomics. Precise identification and understanding of …
A practical framework and online tool for mutational signature analyses show intertissue variation and driver dependencies
A Degasperi, TD Amarante, J Czarnecki, S Shooter… - Nature cancer, 2020 - nature.com
Mutational signatures are patterns of mutations that arise during tumorigenesis. We present
an enhanced, practical framework for mutational signature analyses. Applying these …
an enhanced, practical framework for mutational signature analyses. Applying these …
[HTML][HTML] Systematic analysis of somatic mutations driving cancer: uncovering functional protein regions in disease development
Background Recent advances in sequencing technologies enable the large-scale
identification of genes that are affected by various genetic alterations in cancer. However …
identification of genes that are affected by various genetic alterations in cancer. However …
[HTML][HTML] Protein domain-level landscape of cancer-type-specific somatic mutations
Identifying driver mutations and their functional consequences is critical to our
understanding of cancer. Towards this goal, and because domains are the functional units of …
understanding of cancer. Towards this goal, and because domains are the functional units of …
Big genes are big mutagen targets: A connection to cancerous, spherical cells?
ML Parry, M Ramsamooj, G Blanck - Cancer letters, 2015 - Elsevier
We determined the most commonly mutated genes in five cancer genome atlas (TCGA)
datasets. Many of these genes were extraordinarily large, as are many cancer fusion gene …
datasets. Many of these genes were extraordinarily large, as are many cancer fusion gene …
[HTML][HTML] Design and analysis issues in genome-wide somatic mutation studies of cancer
The availability of the human genome sequence and progress in sequencing and
bioinformatic technologies have enabled genome-wide investigation of somatic mutations in …
bioinformatic technologies have enabled genome-wide investigation of somatic mutations in …
[HTML][HTML] Analysis of 7,815 cancer exomes reveals associations between mutational processes and somatic driver mutations
Driver mutations are the genetic variants responsible for oncogenesis, but how specific
somatic mutational events arise in cells remains poorly understood. Mutational signatures …
somatic mutational events arise in cells remains poorly understood. Mutational signatures …